Open qfaber opened 1 year ago
Hi @qfaber , we are so excited that you are using EUKulele
! So sorry for the trouble with BUSCO
. First question: is it important to you to have the BUSCO
steps done? If not, I've added a flag to ignore those steps, because of how often that particular piece of the pipeline was problematic. If so, we can talk other potential solutions!
Yes, it is. It seems to be running fine now- I'm getting output folders for taxonomy, but not folders for core_taxonomy or busco_assessment
Hello @qfaber - EUKulele has completed without the BUSCO steps, you mean? If you could send the output messages it got to, that would help with diagnosing. Thanks!
Yes, that's what I mean. I attached the output- it ran for several hours on the final step without doing anything, maybe that was the issue. I can also send error logs if that is helpful. Thanks!
From: akrinos @.> Sent: Tuesday, January 17, 2023 5:46 PM To: AlexanderLabWHOI/EUKulele @.> Cc: Faber,Quincy L @.>; Mention @.> Subject: Re: [AlexanderLabWHOI/EUKulele] Busco issue (Issue #49)
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Hello @qfaberhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fqfaber&data=05%7C01%7Cqfaber%40ufl.edu%7C5acc81b1f5dc4201520b08daf8dca6ea%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638095923824356168%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dESPYwc%2BX%2FEpPeKdq4x0ts6ZngiGNmNSjEGgT1Q5hgc%3D&reserved=0 - EUKulele has completed without the BUSCO steps, you mean? If you could send the output messages it got to, that would help with diagnosing. Thanks!
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EUKulele --sample_dir /media/racheljoyce/HDD2/meta_euk/euk_bins -m mags
Running EUKulele with command line arguments, as no valid configuration file was provided. Setting things up... Specified reference directory, reference FASTA, and protein map/taxonomy table not found. Using database in location: ./marmmetsp. Found database folder for ./marmmetsp in current directory; will not re-download. Creating a diamond reference from database files... Diamond database file already created; will not re-create database. Aligning to reference database... Aligning sample all_2014.5.fa... Aligning sample near-ice_2015.4.fa... Aligning sample near-ice_2015.8.fa... Aligning sample englacial_2015.2.fa... Aligning sample near-ice_2015.10.fa... Aligning sample all_2014.1.fa... Aligning sample all_2014.7.fa... Aligning sample wca_2015.2.fa... Aligning sample near-ice_2015.1.fa... Aligning sample englacial_2015.1.fa... Aligning sample near-ice_2015.7.fa... Aligning sample near-ice_2015.6.fa... Diamond process exited for sample near-ice_2015.1.fa. Diamond process exited for sample all_2014.1.fa. Aligning sample near-ice_2015.9.fa... Aligning sample wca_2014.6.fa... Diamond process exited for sample englacial_2015.2.fa. Aligning sample wca_2014.3.fa... Diamond process exited for sample near-ice_2015.8.fa. Aligning sample all_2014.4.fa... Diamond process exited for sample englacial_2015.1.fa. Aligning sample wca_2014.2.fa... Diamond process exited for sample near-ice_2015.7.fa. Aligning sample near-ice_2015.12.fa... Diamond process exited for sample all_2014.7.fa. Aligning sample wca_2014.4.fa... Diamond process exited for sample near-ice_2015.4.fa. Aligning sample wca_2015.1.fa... Diamond process exited for sample all_2014.5.fa. Aligning sample near-ice_2015.14.fa... Diamond process exited for sample near-ice_2015.10.fa. Aligning sample near-ice_2015.13.fa... Diamond process exited for sample near-ice_2015.6.fa. Aligning sample near-ice_2015.3.fa... Diamond process exited for sample wca_2015.2.fa. Aligning sample near-ice_2015.2.fa... Diamond process exited for sample near-ice_2015.9.fa. Aligning sample wca_2014.5.fa... Diamond process exited for sample wca_2015.1.fa. Aligning sample near-ice_2015.11.fa... Diamond process exited for sample near-ice_2015.12.fa. Aligning sample near-ice_2015.15.fa... Diamond process exited for sample near-ice_2015.13.fa. Aligning sample all_2014.6.fa... Diamond process exited for sample near-ice_2015.3.fa. Aligning sample all_2014.3.fa... Diamond process exited for sample wca_2014.3.fa. Aligning sample englacial_2015.3.fa... Diamond process exited for sample near-ice_2015.14.fa. Aligning sample wca_2014.1.fa... Diamond process exited for sample wca_2014.2.fa. Aligning sample near-ice_2014.1.fa... Diamond process exited for sample wca_2014.6.fa. Aligning sample near-ice_2015.5.fa... Diamond process exited for sample near-ice_2015.2.fa. Aligning sample all_2014.2.fa... Diamond process exited for sample wca_2014.4.fa. Diamond process exited for sample all_2014.4.fa. Diamond process exited for sample wca_2014.5.fa. Diamond process exited for sample near-ice_2015.11.fa. Diamond process exited for sample all_2014.6.fa. Diamond process exited for sample englacial_2015.3.fa. Diamond process exited for sample wca_2014.1.fa. Diamond process exited for sample near-ice_2015.15.fa. Diamond process exited for sample all_2014.2.fa. Diamond process exited for sample all_2014.3.fa. Diamond process exited for sample near-ice_2014.1.fa. Diamond process exited for sample near-ice_2015.5.fa. Performing taxonomic estimation steps... Performing taxonomic visualization steps...
The taxonomy estimation steps completed successfully with the dialog you attached?
Yes, for each sample i got files labelled samplename-estimated-taxonomy.out
From: akrinos @.> Sent: Tuesday, January 17, 2023 7:27 PM To: AlexanderLabWHOI/EUKulele @.> Cc: Faber,Quincy L @.>; Mention @.> Subject: Re: [AlexanderLabWHOI/EUKulele] Busco issue (Issue #49)
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The taxonomy estimation steps completed successfully with the dialog you attached?
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@qfaber sorry for not following up on this. Could you send error logs if you're still having these issues with it? thanks!
Hi @qfaber - let me know if you still need help with EUKulele? Else I'll close up this issue. Thanks!
Hi, I am unable to install the recommended version of Busco via conda and the code is no longer available else so I have a newer version: 5.4.3. I ran EUKulele and I don't think busco worked with the latest version- is there a way I can fix this? Thanks!